MolNFT v1 · #81934 · protein
Crystal structure of SCSKP1-SCCDC4-PSIC1 peptide complex
3V7D · Suppressor of kinetochore protein 1: “Crystal structure of SCSKP1-SCCDC4-PSIC1 peptide complex”. X-ray diffraction, 12 pockets (best druggability 0.81). MolNFT v1 #81934 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3V7D
- Type
- protein
- Length
- 1,185 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Suppressor of kinetochore protein 1; Cell division control protein 4; Protein SIC1
- UniProt
- P52286, P07834, P38634
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 24% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Suppressor of kinetochore protein 1 | protein | 139 | 54% helix, 9% strand | P52286 |
| B | Cell division control protein 4 | protein | 450 | 16% helix, 44% strand | P07834 |
| C | Suppressor of kinetochore protein 1 | protein | 139 | 53% helix, 10% strand | P52286 |
| D | Cell division control protein 4 | protein | 447 | 16% helix, 45% strand | P07834 |
| E | Protein SIC1 | protein | 10 | 0% helix, 0% strand | P38634 |
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.81 | 0.82 | 85 | empty |
| 2 | 1038 | 0.81 | 0.82 | 80 | empty |
| 3 | 73 | 0.41 | 0.79 | 22 | empty |
| 4 | 67 | 0.39 | 0.79 | 16 | empty |
| 5 | 81 | 0.37 | 0.76 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1553 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1547 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 629 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 610 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 3V7D · Crystal Structure of ScSkp1-ScCdc4-pSic1 peptide complex · the same entry in another collection · chain E against E, TM-score 1.00
- P07834 · AlphaFold monomer V2.0 prediction for cell division control protein 4 (P07834) · a predicted model of the same protein · chain B against A, TM-score 1.00
- P52286 · AlphaFold monomer V2.0 prediction for suppressor of kinetochore protein 1 (P52286) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P38634 · AlphaFold monomer V2.0 prediction for protein SIC1 (P38634) · a predicted model of the same protein · chain E against A, TM-score 0.38
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P52286
- Every structure of UniProt P07834
- Every structure of UniProt P38634
- Elsewhere: RCSB PDB 3V7D · PDBe 3V7D · UniProt P52286 · UniProt P07834 · UniProt P38634
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